After the events in the final mission at the Collector Base, you will be given a choice with what to do with the base itself: save it for research which will be used by Cerberus or destroy it once and for all.
Choice: Save or Destroy the Collector Base
After fighting your way through the Collector Base during the suicide mission, and killing the Human-Reaper final boss, you will be patched through to the Illusive Man who will try to convince you to spare the Base for Cerberus’s research. Your decision may well depend on your chosen morality for your playthrough as each decision results in either Paragon or Renegade points. Destroying the base results in Paragon points and saving it will net you Renegade points.
Save the Collector Base
If you choose to save the Base for research, you will receive the Reaper Brain War Asset during Mass Effect 3 which has an EMS score of 110. Furthermore, dialogue will differ with notably the Illusive Man and Jack during the events of Mass Effect 3. One thing to note is should your final EMS score fall below 1750, you will only have one choice for the ending of Mass Effect 3 so be sure to gain enough EMS score if you want greater options.
Destroy the Collector Base
If you choose to destroy the Base, you will anger the Illusive Man firstly and secondly you will receive the Reaper Heart War Asset during Mass Effect 3 which as an EMS value of 100. Again, dialogue will differ with the Illusive Man and Jack and some of the crew of the Normandy. Finally, you will be limited to only one choice for the ending of Mass Effect 3 if your EMS value falls below 1750 and you destroyed the base.